5JEA

Structure of a cytoplasmic 11-subunit RNA exosome complex including Ski7, bound to RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of a Cytoplasmic 11-Subunit RNA Exosome Complex.

Kowalinski, E.Kogel, A.Ebert, J.Reichelt, P.Stegmann, E.Habermann, B.Conti, E.

(2016) Mol Cell 63: 125-134

  • DOI: 10.1016/j.molcel.2016.05.028
  • Primary Citation of Related Structures:  
    5JEA

  • PubMed Abstract: 
  • The RNA exosome complex associates with nuclear and cytoplasmic cofactors to mediate the decay, surveillance, or processing of a wide variety of transcripts. In the cytoplasm, the conserved core of the exosome (Exo10) functions together with the conserved Ski complex ...

    The RNA exosome complex associates with nuclear and cytoplasmic cofactors to mediate the decay, surveillance, or processing of a wide variety of transcripts. In the cytoplasm, the conserved core of the exosome (Exo10) functions together with the conserved Ski complex. The interaction of S. cerevisiae Exo10 and Ski is not direct but requires a bridging cofactor, Ski7. Here, we report the 2.65 Å resolution structure of S. cerevisiae Exo10 bound to the interacting domain of Ski7. Extensive hydrophobic interactions rationalize the high affinity and stability of this complex, pointing to Ski7 as a constitutive component of the cytosolic exosome. Despite the absence of sequence homology, cytoplasmic Ski7 and nuclear Rrp6 bind Exo10 using similar surfaces and recognition motifs. Knowledge of the interacting residues in the yeast complexes allowed us to identify a splice variant of human HBS1-Like as a Ski7-like exosome-binding protein, revealing the evolutionary conservation of this cytoplasmic cofactor.


    Organizational Affiliation

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany. Electronic address: conti@biochem.mpg.de.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP45 A305Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP45YDR280WD9954.1
Find proteins for Q05636 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q05636 
Go to UniProtKB:  Q05636
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component SKI6 B249Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SKI6ECM20RRP41YGR195WG7587
Find proteins for P46948 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P46948 
Go to UniProtKB:  P46948
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP43 C394Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP43YCR035CYCR35CYCR522
Find proteins for P25359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25359 
Go to UniProtKB:  P25359
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP46 D226Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP46YGR095C
Find proteins for P53256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53256 
Go to UniProtKB:  P53256
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP42 E268Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP42YDL111C
Find proteins for Q12277 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12277 
Go to UniProtKB:  Q12277
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component MTR3 F250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MTR3YGR158CG6676
Find proteins for P48240 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P48240 
Go to UniProtKB:  P48240
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP40 G244Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP40YOL142W
Find proteins for Q08285 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08285 
Go to UniProtKB:  Q08285
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component RRP4 H316Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP4YHR069C
Find proteins for P38792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38792 
Go to UniProtKB:  P38792
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex component CSL4 I295Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CSL4SKI4YNL232WN1154
Find proteins for P53859 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53859 
Go to UniProtKB:  P53859
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Exosome complex exonuclease DIS3 J1005Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DIS3RRP44YOL021CO2197
EC: 3.1.13 (PDB Primary Data), 3.1.26 (PDB Primary Data)
Find proteins for Q08162 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08162 
Go to UniProtKB:  Q08162
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Superkiller protein 7,Endolysin K279Saccharomyces cerevisiae S288CEscherichia virus T4
This entity is chimeric
Mutation(s): 0 
Gene Names: SKI7YOR076CYOR29-27E
EC: 3.2.1.17
Find proteins for Q08491 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08491 
Go to UniProtKB:  Q08491
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 12
MoleculeChainsLengthOrganismImage
RNA (29-MER)R46synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.08α = 90
b = 182.53β = 90
c = 250.55γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
ERCGermany294371
DFGGermanySFB646
DFGGermanySFB1035
DFGGermanyGRK1721
DFGGermanyFOR1680
DFGGermanyCIPSM

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-13
    Type: Initial release
  • Version 1.1: 2016-08-24
    Changes: Atomic model, Database references